Hi all,
Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects?
I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot.
To repeat the error message, I tried the following command which is called by make_average_subject and found all my subjects shoot this error.
mri_vol2vol --mov 1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm 1173622/mri/transforms/talairach.m3z --o /tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest
I found another same question asked before, but no answer. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024064.html
Any hint or help will be appreciated. Thank you.
This error may come from regio_read_mincxfm function in registerio.c. Does this mean something wrong in recon-all?
I forgot to mention that FreeSurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.song@gmail.com wrote:
Hi all,
Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects?
I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot.
To repeat the error message, I tried the following command which is called by make_average_subject and found all my subjects shoot this error.
mri_vol2vol --mov 1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm 1173622/mri/transforms/talairach.m3z --o /tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest
I found another same question asked before, but no answer. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024064.html
Any hint or help will be appreciated. Thank you.
-- Xiaowei Song
sorry, I don't understand. What was the error? I don't see one in this email. Can you send us the actual screen output?
cheers Bruce On Thu, 7 Mar 2013, Xiaowei Song wrote:
This error may come from regio_read_mincxfm function in registerio.c.Does this mean something wrong in recon-all?
I forgot to mention that FreeSurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.song@gmail.com wrote: Hi all,
Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects?
I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot.
To repeat the error message, I tried the following command which is called by make_average_subject and found all my subjects shoot this error.
mri_vol2vol --mov 1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm 1173622/mri/transforms/talairach.m3z --o /tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest
I found another same question asked before, but noanswer. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024 064.html
Any hint or help will be appreciated. Thank you.
-- Xiaowei Song
-- Xiaowei Song
Sorry, I did not make it clear.
In make_average_volume.log, the error message is:
1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o /data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh --interp nearest ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z does not start as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz ERROR: mri_vol2vol failed.
On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
sorry, I don't understand. What was the error? I don't see one in this email. Can you send us the actual screen output?
cheers Bruce
On Thu, 7 Mar 2013, Xiaowei Song wrote:
This error may come from regio_read_mincxfm function in registerio.c.Does
this mean something wrong in recon-all?
I forgot to mention that FreeSurfer version is freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0
On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song dawnwei.song@gmail.com wrote: Hi all,
Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects?
I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot.
To repeat the error message, I tried the following command which is called by make_average_subject and found all my subjects shoot this error.
mri_vol2vol --mov 1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/**mni305.cor.mgz --xfm 1173622/mri/transforms/**talairach.m3z --o /tmp/make_average_vol-tmp-**164320_seg-1173622.mgh --interp nearest
I found another same question asked before, but noanswer. https://mail.nmr.**mgh.harvard.edu/pipermail//**freesurfer/2012-May/024https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/024 064.html
Any hint or help will be appreciated. Thank you.
-- Xiaowei Song
-- Xiaowei Song
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
what was your command line? On Thu, 7 Mar 2013, Xiaowei Song wrote:
Sorry, I did not make it clear. In make_average_volume.log, the error message is:
1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o /data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh --interp nearest ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z does not start as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz ERROR: mri_vol2vol failed.
On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: sorry, I don't understand. What was the error? I don't see one in this email. Can you send us the actual screen output?
cheers Bruce On Thu, 7 Mar 2013, Xiaowei Song wrote: This error may come from regio_read_mincxfm function in registerio.c.Does this mean something wrong in recon-all? I forgot to mention that FreeSurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song <dawnwei.song@gmail.com> wrote: Hi all, Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects? I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot. To repeat the error message, I tried the following command which is called by make_average_subject and found all my subjects shoot this error. mri_vol2vol --mov 1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm 1173622/mri/transforms/talairach.m3z --o /tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest I found another same question asked before, butnoanswer. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0 24 064.html Any hint or help will be appreciated. Thank you. -- Xiaowei Song -- Xiaowei SongThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Xiaowei Song
Thanks for your help.
My command line is make_average_subject --out avgGrp139 --subjects `cat script/subjects.id` --xform talairach.m3z
On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
what was your command line?
On Thu, 7 Mar 2013, Xiaowei Song wrote:
Sorry, I did not make it clear.
In make_average_volume.log, the error message is:
1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/**aseg.mgz --targ /usr/local/freesurfer/average/**mni305.cor.mgz --xfm /data/lis9/fs/x/1173622/mri/**transforms/talairach.m3z --o /data/lis9/fs/x/avgGrp139/tmp/**make_average_vol-tmp-55832/** seg-1173622.mgh --interp nearest ERROR: /data/lis9/fs/x/1173622/mri/**transforms/talairach.m3z does not start as 'MNI Transform File'/spin1/users/lis9/fs/dcm.**mprage.mgz ERROR: mri_vol2vol failed.
On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: sorry, I don't understand. What was the error? I don't see one in this email. Can you send us the actual screen output?
cheers Bruce On Thu, 7 Mar 2013, Xiaowei Song wrote: This error may come from regio_read_mincxfm function in registerio.c.Does this mean something wrong in recon-all? I forgot to mention that FreeSurfer version is freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song <dawnwei.song@gmail.com> wrote: Hi all, Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects? I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot. To repeat the error message, I tried the following command which is called by make_average_subject and found all my subjects shoot this error. mri_vol2vol --mov 1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/**mni305.cor.mgz --xfm 1173622/mri/transforms/**talairach.m3z --o /tmp/make_average_vol-tmp-**164320_seg-1173622.mgh --interp nearest I found another same question asked before, butnoanswer.https://mail.nmr.**mgh.harvard.edu/pipermail//**freesurfer/2012-May/0https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0 24 064.html
Any hint or help will be appreciated. Thank you. -- Xiaowei Song -- Xiaowei SongThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- Xiaowei Song
The xform has to be linear in the xfm format. The m3z cannot be used. doug
On 03/07/2013 06:44 PM, Xiaowei Song wrote:
Thanks for your help.
My command line is make_average_subject --out avgGrp139 --subjects `cat script/subjects.id http://subjects.id` --xform talairach.m3z
On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
what was your command line? On Thu, 7 Mar 2013, Xiaowei Song wrote: Sorry, I did not make it clear. In make_average_volume.log, the error message is: 1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o /data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh --interp nearest ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z does not start as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz ERROR: mri_vol2vol failed. On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: sorry, I don't understand. What was the error? I don't see one in this email. Can you send us the actual screen output? cheers Bruce On Thu, 7 Mar 2013, Xiaowei Song wrote: This error may come from regio_read_mincxfm function in registerio.c.Does this mean something wrong in recon-all? I forgot to mention that FreeSurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song <dawnwei.song@gmail.com <mailto:dawnwei.song@gmail.com>> wrote: Hi all, Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects? I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot. To repeat the error message, I tried the following command which is called by make_average_subject and found all my subjects shoot this error. mri_vol2vol --mov 1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm 1173622/mri/transforms/talairach.m3z --o /tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest I found another same question asked before, butnoanswer. https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0 24 064.html Any hint or help will be appreciated. Thank you. -- Xiaowei Song -- Xiaowei Song The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Xiaowei Song-- Xiaowei Song
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you, doug, I will try xfm!
On Thu, Mar 7, 2013 at 7:03 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The xform has to be linear in the xfm format. The m3z cannot be used. doug
On 03/07/2013 06:44 PM, Xiaowei Song wrote:
Thanks for your help.
My command line is make_average_subject --out avgGrp139 --subjects `cat script/subjects.id http://subjects.id` --xform talairach.m3z
On Thu, Mar 7, 2013 at 6:15 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
what was your command line? On Thu, 7 Mar 2013, Xiaowei Song wrote: Sorry, I did not make it clear. In make_average_volume.log, the error message is: 1/139 1173622 aseg Sat Feb 23 02:26:02 EST 2013 mri_vol2vol --mov /data/lis9/fs/x/1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z --o/data/lis9/fs/x/avgGrp139/tmp/make_average_vol-tmp-55832/seg-1173622.mgh
--interp nearest ERROR: /data/lis9/fs/x/1173622/mri/transforms/talairach.m3z does not start as 'MNI Transform File'/spin1/users/lis9/fs/dcm.mprage.mgz ERROR: mri_vol2vol failed. On Thu, Mar 7, 2013 at 5:49 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: sorry, I don't understand. What was the error? I don't see one in this email. Can you send us the actual screen output? cheers Bruce On Thu, 7 Mar 2013, Xiaowei Song wrote: This error may come from regio_read_mincxfm function in registerio.c.Does this mean something wrong in recon-all? I forgot to mention that FreeSurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 On Thu, Mar 7, 2013 at 5:34 PM, Xiaowei Song <dawnwei.song@gmail.com <mailto:dawnwei.song@gmail.com>> wrote: Hi all, Did you encounter the error message talairach.m3z does not start as 'MNI Transform File' when making average of subjects? I checked all the recon-all.log file and did not find error, but when running make_average_subject after recon-all, then this error shoot. To repeat the error message, I tried the following command which is called by make_average_subject and found all my subjects shoot this error. mri_vol2vol --mov 1173622/mri/aseg.mgz --targ /usr/local/freesurfer/average/mni305.cor.mgz --xfm 1173622/mri/transforms/talairach.m3z --o /tmp/make_average_vol-tmp-164320_seg-1173622.mgh --interp nearest I found another same question asked before, butnoanswer.https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2012-May/0
24 064.html Any hint or help will be appreciated. Thank you. -- Xiaowei Song -- Xiaowei Song The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Xiaowei Song-- Xiaowei Song
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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